I agree with the comments from Peace River. If you are making your own overflow as shown in the picture, you have a little more flexibility on where to place the holes. The depth of the primary overflow is critical as it will set the water level in the overflow box. The secondary or emergency overflow can be deeper and just extend it with a short section of pipe as needed. The full siphon can be deeper in the box. I would do a mock-up of the elbows inside the box before drilling to decide on where to place the holes. If the elbows are threaded into the bulkheads, they need to be far enough apart to turn them without striking each other.
One other bit of advice on drilling is to apply heavy duct tape on the back side of the hole and have it fully supported on the back side with a block of wood on a solid surface so that when it breaks through you minimize any chipping of the glass on the edge of the hole. Go slow as has been previously recommended with only light pressure on the drill.